Changes for page Access data with ImageJ

Last modified by fwilde on 2018/12/18 12:01
From version 8.1
edited by fwilde
on 2016/07/28 08:40
Change comment: There is no comment for this version
To version 11.1
edited by fwilde
on 2016/09/15 09:17
Change comment: There is no comment for this version

Summary

Details

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Content
... ... @@ -7,10 +7,11 @@
7 7  
8 8  Each image contains a header consisting of the information needed to open the binary raw file. To read the header open the first line of the dataset (e.g. with the {{code language="none"}}head{{/code}} command in Linux or in an editor). The header information is subdivided with underscore symbols, like e.g. {{code language="none"}}PC_2_U_2000_2000_{{/code}}. The first item describes on what kind of computer the data was generated. The second item shows the dimensionailty of the data (2 for an image). The next item is a letter (either B U I L or F ) and describes the data type. A list of te data types can be found in the table below. The last items give the length of the dataset in each dimension. The total header length is not fixed and generally depends on the image dimensions.and count all letters until the carriage return. Add 2 to this number (carriage return has two letters) and this is the header length - e.g. {{code language="none"}}PC_2_U_2000_2000_{{/code}} has 17 letters ansd thus results in a header length of 19.
9 9  
10 +(% class="wrapped" %)
10 10  |=(((
11 11  suffix
12 12  )))|=(((
13 -data type
14 +ImageJ data type
14 14  )))|=(((
15 15  header tag
16 16  )))
... ... @@ -17,7 +17,7 @@
17 17  |(((
18 18  
19 19  )))|(((
20 -8 bit integer
21 +8 bit
21 21  )))|(((
22 22  B
23 23  )))
... ... @@ -24,7 +24,7 @@
24 24  |(((
25 25  .img .dar .ref
26 26  )))|(((
27 -16 bit unsigned integer
28 +16 bit Unsigned
28 28  )))|(((
29 29  U
30 30  )))
... ... @@ -31,7 +31,7 @@
31 31  |(((
32 32  
33 33  )))|(((
34 -16 bit integer
35 +16 bit Signed
35 35  )))|(((
36 36  I
37 37  )))
... ... @@ -38,7 +38,7 @@
38 38  |(((
39 39  
40 40  )))|(((
41 -32 bit integer
42 +32 bit Signed
42 42  )))|(((
43 43  L
44 44  )))
... ... @@ -45,7 +45,7 @@
45 45  |(((
46 46  .sli .sin .sis
47 47  )))|(((
48 -32 bit float
49 +32 bit Real
49 49  )))|(((
50 50  F
51 51  )))
... ... @@ -52,8 +52,14 @@
52 52  
53 53  = {{id name="AccessdatawithImageJ-Importrawdatadirectly"/}}Import raw data directly =
54 54  
55 -With ImageJ you can import binary data directly using {{code language="none"}}File > Import > Raw...{{/code}}. To import the raw data directly, read the header of the file you want to open, enter the according values and check the box {{code language="none"}}Little-endian byte order{{/code}}. You can choose to {{code language="none"}}Open all files in folder{{/code}} if you want to open a stack with all file in a folder. **Attention**: {{code language="none"}}Use virtual stack{{/code}} does not work with this kind of import. To open a virtual stack you need to use our plugins.
56 +With ImageJ you can import binary data directly using {{code language="none"}}File > Import > Raw...{{/code}}. To import the raw data directly, read the header of the file you want to open, enter the values:
56 56  
58 +* Image type (see table ImageJ data type)
59 +* Width and height (last two numbers in header)
60 +* Offset to first image (i.e. header length)
61 +
62 +and check the box {{code language="none"}}Little-endian byte order{{/code}}. You can choose to {{code language="none"}}Open all files in folder{{/code}} if you want to open a stack with all file in a folder. **Attention**: {{code language="none"}}Use virtual stack{{/code}} does not work with this kind of import. To open a virtual stack you need to use our plugins.
63 +
57 57  [[image:attach:imagej_raw_import.png||height="250"]]
58 58  
59 59  = {{id name="AccessdatawithImageJ-UsetheImageJplugins"/}}Use the ImageJ plugins =
... ... @@ -69,11 +69,13 @@
69 69  
70 70  = {{id name="AccessdatawithImageJ-Downloads"/}}Downloads =
71 71  
72 -{{panel titleBGColor="blue" title="ImageJ Plugins" borderColor="blue" titleColor="white"}}
79 +{{panel borderColor="blue" titleColor="white" titleBGColor="blue" title="ImageJ Plugins"}}
73 73  **Binary files to copy to your plugin folder:**
74 74  
75 75  [[attach:HandleExtraFileTypes.jar]]
76 76  
84 +[[attach:HandleExtraFileTypes.class]]
85 +
77 77  [[attach:read_dat.class]]
78 78  
79 79  **Source code:**
Confluence.Code.ConfluencePageClass[0]
Id
... ... @@ -1,1 +1,1 @@
1 -37489288
1 +42350827
URL
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1 -https://confluence.desy.de/spaces/P5I/pages/37489288/Access data with ImageJ
1 +https://confluence.desy.de/spaces/P5I/pages/42350827/Access data with ImageJ